| Summary | Assembly | Insert sizes | Busco | Bracken (Illumina) | MLST | Serotypes | Software |
| User | mhoeppner |
| Date | 2025-02-07 08:17:45.726670 |
| Pipeline version | 0.9.6 |
| Command line call | nextflow run /home/mhoeppner/git/bio-raum/gabi/main.nf -profile lsh --input samples.csv --run_name Test -resume |
| Work directory | /work_syn/ngs/pipelines/gabi/test/work |
| Sample | StatusThe overall analysis status: pass: ok to use, warn: potential issues found, fail: most probably not usable |
Best-guess taxonThe highest scoring taxon using kmer matching (S/MASH) |
Reference genomeThe highest matching hit in RefSeq to this assembly |
AssemblyInformation about this assembly |
Mean coverageMean coverage of reads mapped back to the assembly - bigger is better |
Coverage 40X (%)Percentage of assembly covered at 40X or more |
Read qualityQuality metrics of reads after trimming |
ContaminationIndicators of contamination |
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Assembly | % Cov | Size (Mb) | #ContigsThe number of chromosomal contigs, i.e. without plasmids. |
N50 (Kb)The size of contigs (>=)in which 50% of the assembly are represented. |
Gene space (%)The fraction of broadly conserved genes fully covered in this assembly (BUSCO). |
GC (%)GC content of the assembly. Deviations from the species default are highlighted in orange (mild) and red (strong, something likely wrong) |
Total | ILM | ONT | HiFi | TotalAcross all sequencing technologies |
ILMIllumina reads 40X |
ONTONT reads 40X |
HiFiPacbio reads 40X |
ILM Q30 (%)Fraction of Illumina reads above Q30. |
ONT Q15 (#)Number of ONT reads above Q15. |
ONT N50 (bp)N50 of ONT reads |
Confindr (%)Based on sequence variation; not 100% reliable for ONT data. |
Taxa >10% | |||
| SAMEA2707760_Ecoli | pass | Escherichia coli | GCF_002176515.1 | 98.2 | 5.27 | 136 | 160.67 | 100.0 | 50.34 | 87.68 | 87.68 | - | - | 100 | 100 | - | - | 90.0 | - | - | - | 1 |
| Sample | Assembly size (Mb) | Fraction of reference | Ns per 100kb | Largest contig (Kb) | Misassembled contigs | Contigs > 1kb | Contigs > 5kb | Size (Mb) in contigs > 1kb | Size (Mb) in contigs > 5kb |
|---|---|---|---|---|---|---|---|---|---|
| SAMEA2707760_Ecoli | 5.27 | 98.2 | 0.00 | 375.97 | 78 | 106 | 60 | 5.24 | 5.13 |
| Sample | MLST type |
|---|---|
| SAMEA2707760_Ecoli | 296 |
| Sample | MLST type |
|---|---|
| SAMEA2707760_Ecoli | 11 |
| Sample | Serotype |
|---|---|
| SAMEA2707760_Ecoli | O157:H7 |
| Sample | Serotype |
|---|---|
| SAMEA2707760_Ecoli | O157:H7 |
| ABRICATE_RUN | |
| abricate: 1.0.1 | |
| ABRICATE_RUN_ECOLI_VIRULENCE | |
| abricate: 1.0.1 | |
| BCFTOOLS_STATS | |
| bcftools: '1.20' | |
| BRACKEN_BRACKEN | |
| bracken: '2.9' | |
| BUSCO_BUSCO | |
| busco: 5.3.0 | |
| CONFINDR | |
| confindr: 0.7.4 | |
| CUSTOM_DUMPSOFTWAREVERSIONS | |
| python: 3.11.7 | |
| yaml: 5.4.1 | |
| DNAAPLER | |
| dnaapler: 1.1.0 | |
| DOWNLOAD_GENOME | |
| datasets: 16.22.1 | |
| ECTYPER | |
| ectyper: 2.0.0 | |
| FASTP | |
| fastp: 0.23.4 | |
| FASTQC | |
| fastqc: 0.12.1 | |
| HAMRONIZATION_ABRICATE | |
| hamronization: 1.1.4 | |
| HAMRONIZATION_AMRFINDERPLUS | |
| hamronization: 1.1.4 | |
| HAMRONIZATION_SUMMARIZE | |
| hamronization: 1.1.4 | |
| KRAKEN2_KRAKEN2 | |
| kraken2: 2.1.2 | |
| pigz: '2.6' | |
| MLST | |
| mlst: 2.23.0 | |
| MOBSUITE_RECON | |
| mobsuite: 3.1.8 | |
| PROKKA | |
| prokka: 1.14.6 | |
| QUAST | |
| quast: 5.2.0 | |
| SHOVILL | |
| shovill: 1.1.0 | |
| SNIPPY_RUN | |
| snippy: 4.6.0 | |
| SOURMASH_SEARCH | |
| sourmash: 4.8.4 | |
| SOURMASH_SKETCH | |
| sourmash: 4.8.4 | |
| STECFINDER | |
| stecfinder: 1.1.0 | |
| TABIX_TABIX | |
| tabix: '1.20' | |
| Workflow | |
| Nextflow: 24.04.4 | |
| bio-raum/gabi: 0.9.6 | |